Polynucleotides and polypeptides associated with the development of rheumatoid arthritis

ABSTRACT

The present invention is directed to polynucleotides encoding polypeptides associated with the development of rheumatoid arthritis and homologs thereof. The invention further relates to diagnostic and therapeutic methods for utilizing these polynucleotides and polypeptides in the diagnosis, treatment, and/or prevention of rheumatoid arthritis and related disease states. The invention further relates to screening methods for identifying agonists and antagonists of the polynucleotides and polypeptides of the present invention, and compounds identified thereby.

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to U.S. Provisional Patent Application No. 60/337,429, filed Dec. 3, 2001, and hereby expressly incorporated by reference in its entirety.

FIELD OF THE INVENTION

[0002] The present invention provides polynucleotides encoding polypeptides associated with the development and progression of rheumatoid arthritis and homologs thereof. Also provided are vectors, host cells, antibodies, and recombinant and synthetic methods for producing said polypeptides. The invention further relates to diagnostic and therapeutic methods for utilizing these polypeptides in the diagnosis, treatment, and/or prevention of rheumatoid arthritis and related disease states. The invention further relates to screening methods for identifying agonists and antagonists of the polynucleotides and polypeptides of the present invention.

BACKGROUND OF RELATED TECHNOLOGY

[0003] Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by progressive joint destruction. Initial destruction of cartilage and bone is associated with the formation of a pannus, consisting of a hypertrophic synovial membrane containing hyperplastic synoviocytes and an infiltrate of inflammatory cells including T cells, B cells, CD68+macrophages, mast cells, and endothelial cells. The causes of RA are not well understood. Genetic studies have linked expression of specific major histocompatibility complex class II antigens to the development of RA, suggesting the involvement of antigen-specific mechanisms in disease progression (Zanelli et al., Hum. Immunol. 61:1254-1261 (2000)).

[0004] CD4+ T cells are thought to play a key role in initiation and progression of disease. Although many putative self antigens have been proposed, none have been definitively associated with the initiation of disease. Antigen-activated T cells stimulate monocytes, macrophages, and synovial fibroblasts to secrete pro-inflammatory cytokines including interleukin-1 (IL-1), interleukin-6 (IL-6), and TNF-α. These cytokines stimulate synovial fibroblasts, osteoclasts, and chondrocytes to release matrix metalloproteinases (MMPs) that destroy surrounding tissue. Activated CD4+ T cells stimulate osteoclastogenesis that can also contribute to joint damage. The activated T cells also stimulate B cells present in the synovium via the CD40 pathway to differentiate into antibody secreting cells producing rheumatoid factor, which may also contribute to disease pathology.

[0005] Many of the cytokines found in rheumatoid synovium have been directly linked to disease pathology. For example, TNF-α promotes inflammation by inducing secretion of other inflammatory cytokines including IL-1, IL-6, IL-8, GM-CSF, as well as by upregulating adhesion molecule expression on endothelial cells and synovial fibroblasts. These two events promote increased migration of lymphocytes including neutrophils, monocytes, and T cells into the synovium. Neutrophils release elastase and proteases that degrade proteoglycan and contribute to joint destruction. Therapies targeting TNF-α include the use of soluble TNF-α receptor (Etanercept) and neutralizing antibodies specific for TNF-α (Infliximab), and result in a significant decrease in the number of swollen joints, as well as the numbers of T cells and plasma cells in the synovium of RA patients. Such therapies also result in a decrease in the expression of VCAM-1 and IL-1 in the synovium of treated patients (Bathon, et al., New Engl. J. Med. 343:1586-1593 (2000); Lipsky, et al., New Engl. J. Med. 343:1594-1602 (2000); Richard-Miceli, et al., Biodrugs 15:251-259 (2001)).

[0006] IL-1 has also been closely linked to the pathophysiology of RA. IL-1 induces synovial cell proliferation and activates MMP and prostaglandin production in vitro (Mizel et al., Proc. Natl. Acad. Sci. USA 78:2474-2477 (1981)). In several mouse models of arthritis, IL-1 is believed to play a dominant role in cartilage destruction, whereas TNF-α is primarily proinflammatory (Joosten et al., J. Immunol. 163:5049-5055 (1999)). Transgenic mice constitutively expressing human IL-1α in various organs develop a severe polyarthritic phenotype with a predominance of neutrophils and macrophages in the diseased joints (Niki et al., J. Clin. Invest. 107:1127-1135 (2001)). Synovitis developed within two weeks of birth, followed by pannus formation and cartilage destruction within 8 weeks after birth. Treatment of RA patients with a natural inhibitor of IL-1, recombinant human IL-1 receptor antagonist (IL-1Ra), significantly reduced clinical symptoms and the rate of progressive joint damage (Jiang et al., Arthritis Rheum. 43:1001-1009 (2000); Bresnihan et al., Biodrugs 15:87-97 (2001)).

[0007] A number of studies have sought to identify genes whose expression is associated with the development of RA. cDNA microarrays have been used to compare expression profiles between tissue samples derived from RA and inflammatory bowel disease patients. Such studies have found that prominently upregulated genes in RA samples include: IL-6; the MMPs stromelysin-1, collagenase-1, gelatinase A, and human matrix metalloelastase; tissue inhibitors of metalloproteinases, including TIMP-1 and TIMP-3; the adhesion molecule VCAM-1; and chemokines including MCP-1, MIF, and RANTES (Heller et al. Proc. Natl. Acad. Sci. USA 94: 2150-2155 (1997)). Further, a cDNA library has been generated from monocytes obtained from a RA patient with active disease (Stuhlmuller et al., Arthritis Rheum. 43:775-790 (2000)). Genes found to be upregulated in these cells include IL-1α, IL-1β, IL-6, TNF-α, growth-related oncogene α, macrophage inflammatory protein 2, ferritin, α1-antitrypsin, lysozyme, transaldolase, Epstein-Barr virus-encoded RNA 1-associated protein, thrombospondin 1, angiotensin receptor II C-terminal homologue, and RNA polymerase II elongation factor.

[0008] In one study, a cDNA library was generated by subtracting cDNA derived from noninflammatory osteoarthritis (OA) synoviocytes from cDNA derived from cultured RA fibroblastoid synoviocytes (Seki et al., Arthritis Rheum. 41:1356-1364 (1998)). Genes found to be constitutively overexpressed in the rheumatoid synoviocyte line include: chemokine stromal cell-derived factor 1α; adhesion molecule VCAM-1; interferon-inducible 56-kD protein; 2′-5′-oligoadenylate synthetase; Mac-2 binding protein; extracellular matrix components biglycan, lumican, and IGFBP5; and semaphorin VI.

[0009] Studies have also been conducted using suppression subtractive hybridization to identify genes that are highly expressed in RA synovium relative to OA synovium (Justen et al., Mol. Cell Biol. Res. Comm. 3:165-172 (2000)). Genes found to be specifically upregulated in RA synovium include: cytoskeletal γ-actin; the extracellular matrix components fibronectin and collagen IIIα1; superficial zone protein; elongation factor α1; granulin precursor; interferon-γinducible lysosomal thiol reductase; the protease cathepsin B; phospholipase A2 group IIA; and annexin II.

[0010] Accordingly, there is a continuing need to identify genes whose expression is associated with the development and progression of RA. The identification of such genes permits the development of clones expressing such genes, thereby permitting the identification of compounds capable of modulating the activity of such genes and/or their expression products. Such compounds may have therapeutic utility in the diagnosis and/or treatment of RA and related disease states. The present invention is directed to meeting these and other needs.

BRIEF DESCRIPTION OF THE DRAWINGS

[0011]FIGS. 1, 4, 7, 10, 13, 16, 19, 22, 25, 28, 31, 34, 37, 40, 43, 46, 49, 52, 55, 58, 61, 64, 67, 69, 71, 74, 76, 79, 82 and 85 show microarray data for genes of the present invention shown to be upregulated and downregulated in rheumatoid arthritis synovial fluid.

[0012]FIGS. 2, 5, 8, 11, 14, 17, 20, 23, 26, 29, 32, 35, 38, 41, 44, 47, 50, 53, 56, 59, 62, 65, 68, 70, 72, 75, 77, 80, 83 and 86 show polynucleotide sequences for genes of the present invention shown to be upregulated and downregulated in rheumatoid arthritis synovial fluid.

[0013]FIGS. 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, 60, 63, 66, 73, 78, 81, 84 and 87 show amino acid sequences for the expression product of genes of the present invention shown to be upregulated and downregulated in rheumatoid arthritis synovial fluid.

[0014]FIG. 88 shows the regulation of GBP-1 and GBP-5 expression by NFkB.

[0015]FIG. 89 shows the time course of GBP-1 and GBP-5 expression.

[0016]FIG. 90 shows GBP-1 and GBP-5 expression in mouse embryonic fibroblast lines derived from NFkB and IkBα germline knockouts.

[0017]FIG. 91 shows tissue expression patterns of GBP-1 and GBP-5.

[0018]FIG. 92 shows expression of GBP-1 and GBP-5 in resting and stimulated THP-1 monocytes.

[0019]FIG. 93 shows expression of GBP-1 and GBP-5 in resting and stimulated human microvascular endothelial cells.

[0020]FIG. 94 shows expression of GBP-1 and GBP-5 in resting and stimulated fibroblasts derived from rheumatoid arthritis synovium.

[0021]FIG. 95 shows expression of GBP-1 and GBP-5 in resting and stimulated peripheral blood T cells.

SUMMARY OF THE INVENTION

[0022] In one aspect, the present invention is directed to an assay for identifying a compound that modulates the activity of a gene associated with rheumatoid arthritis, including the steps of: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein the nucleic acid sequence of the gene associated with rheumatoid arthritis is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73, and SEQ ID NO:74; (2) contacting the cell expressing the gene associated with rheumatoid arthritis with a test compound; and (3) determining whether the test compound modulates the activity of the gene associated with rheumatoid arthritis. The assay may be cell-based assay or may be a cell-free assay, such as a ligand-binding assay. The test compound desirably modulates the activity of the gene associated with rheumatoid arthritis, may be an antagonist or an agonist of the gene associated with rheumatoid arthritis, and may bind to the gene associated with rheumatoid arthritis. The assay is desirably useful for identifying compounds which are useful for the treatment of rheumatoid arthritis.

[0023] In another aspect, the present invention is directed to an assay for identifying a compound that modulates the activity of a protein associated with rheumatoid arthritis, including the steps of: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein the gene encodes a polypeptide having an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72, and SEQ ID NO:75; (2) contacting the cell expressing the gene associated with rheumatoid arthritis with a test compound; and (3) determining whether the test compound modulates the activity of the protein associated with rheumatoid arthritis. The test compound desirably modulates the activity of the protein associated with rheumatoid arthritis, may be an antagonist or an agonist of the protein associated with rheumatoid arthritis, and may bind to the protein associated with rheumatoid arthritis. The assay is desirably useful for identifying compounds which are useful for the treatment of rheumatoid arthritis.

[0024] In another aspect, the present invention is directed to a method for the treatment of rheumatoid arthritis, including the steps of: (1) identifying a patient suffering from rheumatoid arthritis; and (2) administering to the patient a therapeutically effective amount of a modulator of a gene associated with rheumatoid arthritis, wherein the gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73, and SEQ ID NO:74. The patient is desirably identified as suffering from rheumatoid arthritis by measuring the expression level of the gene associated with rheumatoid arthritis in the patient. The modulator is desirably an antagonist of a gene associated with rheumatoid arthritis.

[0025] In another aspect, the present invention is directed to a method for the treatment of rheumatoid arthritis, including the steps of: (1) identifying a patient suffering from rheumatoid arthritis; and (2) administering to the patient suffering from rheumatoid arthritis a therapeutically effective amount of a modulator of a polypeptide associated with rheumatoid arthritis, wherein the polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72, and SEQ ID NO:75. The patient is desirably identified as suffering from rheumatoid arthritis by measuring the expression level of the polypeptide associated with rheumatoid arthritis. The modulator is desirably an antagonist of a polypeptide associated with rheumatoid arthritis.

[0026] In another aspect, the present invention is directed to a method for the prevention of rheumatoid arthritis, including the steps of: (1) identifying a patient at risk for rheumatoid arthritis; and (2) administering to the patient at risk for rheumatoid arthritis a therapeutically effective amount of a modulator of a gene associated with rheumatoid arthritis, wherein the gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73, and SEQ ID NO:74. The patient is desirably identified as being at risk for rheumatoid arthritis by measuring the expression level of the gene associated with rheumatoid arthritis in the patient.

[0027] In another aspect, the present invention is directed to a method for the prevention of rheumatoid arthritis, including the steps of: (1) identifying a patient at risk for rheumatoid arthritis; and (2) administering to the patient at risk for rheumatoid arthritis a therapeutically effective amount of a modulator of a polypeptide associated with rheumatoid arthritis, wherein the polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72, and SEQ ID NO:75. The patient is desirably identified as being at risk for rheumatoid arthritis by measuring the expression level of the polypeptide associated with rheumatoid arthritis in the patient.

[0028] In another aspect, the present invention is directed to a compound useful for the treatment of rheumatoid arthritis, wherein the compound is identified by: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein the gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73, and SEQ ID NO:74; (2) contacting the cell expressing the gene associated with rheumatoid arthritis with the compound; and (3) determining whether the compound modulates the activity of the gene associated with rheumatoid arthritis.

[0029] In another aspect, the present invention is directed to a compound useful for the treatment of rheumatoid arthritis, wherein the compound is identified by: (1) providing a cell expressing a polypeptide associated with rheumatoid arthritis, wherein the polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72, and SEQ ID NO:75; (2) contacting the cell expressing the polypeptide associated with rheumatoid arthritis with the compound; and (3) determining whether the compound modulates the activity of the polypeptide associated with rheumatoid arthritis.

DETAILED DESCRIPTION OF THE INVENTION

[0030] The present invention is directed to the identification of genes associated with Rheumatoid Arthritis (RA). Such genes and their polypeptide expression products are hereinafter referred to as “RA-associated genes and polypeptides”. In the present invention, RA-associated genes and polypeptides have been identified by probing Affymetrix chips (describe) with mRNA derived from the synovia of RA patients, as set forth in Section A of “Materials and Methods”, hereinbelow. Gene expression patterns were compared to those obtained using mRNA derived from synovia of control joint trauma patients. Several genes were identified as having significantly increased expression in the RA synovium relative to the controls, as further described hereinbelow. Several genes have also been identified as having significantly decreased expression in the RA synovium relative to the controls, as further described hereinbelow.

[0031] The present invention provides synthetic methods for producing RA-associated genes and polypeptides. Also provided are diagnostic methods for detecting diseases, disorders, and/or conditions related to RA-associated genes and polypeptides, and therapeutic methods for treating such diseases, disorders, and/or conditions. The invention further relates to screening methods for identifying binding partners of RA-associated genes and polypeptides.

[0032] Examples of functional assays useful in the present invention include LPS-induced TNFα and TNFα-induced IL-1β secretion by THP-1 monocytes, anti-CD3/anti-CD28-induced IL-2 secretion by Jurkat T cells, TNFα-induced IL-1β secretion by synovial fibroblasts, TNFα-induced E-selectin expression by endothelial cells, and anti-CD40-induced homotypic aggregation of Raji B cells.

[0033] One of skill in the art will recognize that RA-associated genes and polypeptides of the present invention are desirably murine or human, but may be from any suitable organism. The genomic and protein sequences of RA-associated genes and polypeptides from these organisms are readily accessed via Genbank or The National Center for Biotechnology Information.

[0034] Further, derivatives and homologues of RA-associated genes and polypeptides may be used in the present invention. For example, nucleic acid sequences of RA-associated genes of the present invention may be altered by substitutions, additions, or deletions that provide for functionally equivalent-conservative variants of such genes. Further, one or more amino acid residues within the amino acid sequence of RA-associated polypeptides can be substituted by another amino acid of similar properties, such as, for example, positively charged amino acids (arginine, lysine, and histidine); negatively charged amino acids (aspartate and glutamate); polar neutral amino acids; and non-polar amino acids.

[0035] Other conservative amino acid substitutions can be taken from the Table 1, below. TABLE 1 Conservative Amino Acid Replacements For Amino Acid Code Replace with any of: Alanine A D-Ala, Gly, beta-Ala, L-Cys, D-Cys Arginine R D-Arg, Lys, D-Lys, homo-Arg, D-homo-Arg, Met, Ile, D-Met, D-Ile, Orn, D-Orn Asparagine N D-Asn, Asp, D-Asp, Glu, D-Glu, Gln, D-Gln Aspartic Acid D D-Asp, D-Asn, Asn, Glu, D-Glu, Gln, D-Gln Cysteine C D-Cys, S-Me-Cys, Met, D-Met, Thr, D-Thr Glutamine Q D-Gln, Asn, D-Asn, Glu, D-Glu, Asp, D-Asp Glutamic Acid E D-Glu, D-Asp, Asp, Asn, D-Asn, Gln, D-Gln Glycine G Ala, D-Ala, Pro, D-Pro, β-Ala, Acp Isoleucine I D-Ile, Val, D-Val, Leu, D-Leu, Met, D-Met Leucine L D-Leu, Val, D-Val, Met, D-Met Lysine K D-Lys, Arg, D-Arg, homo-Arg, D-homo-Arg, Met, D-Met, Ile, D-Ile, Orn, D-Orn Methionine M D-Met, S-Me-Cys, Ile, D-Ile, Leu, D-Leu, Val, D-Val Phenylalanine F D-Phe, Tyr, D-Thr, L-Dopa, His, D-His, Trp, D-Trp, Trans-3,4, or 5-phenylproline, cis-3,4, or 5-phenylproline Proline P D-Pro, L-1-thioazolidine-4-carboxylic acid, D- or L-1-oxazolidine-4-carboxylic acid Serine S D-Ser, Thr, D-Thr, allo-Thr, Met, D-Met, Met(O), D-Met(O), L-Cys, D-Cys Threonine T D-Thr, Ser, D-Ser, allo-Thr, Met, D-Met, Met(O), D-Met(O), Val, D-Val Tyrosine Y D-Tyr, Phe, D-Phe, L-Dopa, His, D-His Valine V D-Val, Leu, D-Leu, Ile, D-Ile, Met, D-Met

[0036] Other analogs within the present invention are those with modifications which increase protein stability; such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the protein sequence. Also included are analogs that include residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., β or γ amino acids.

[0037] RA-associated polypeptides of the present invention may be modified by, for example, phosphorylation, sulfation, acylation, or other protein modifications. They may also be modified with a label capable of providing a detectable signal, either directly or indirectly, including, but not limited to, radioisotopes and fluorescent compounds.

[0038] It will be apparent to one of skill in the art that conventional screening assays may be used in methods of the present invention for the identification of modulators of RA-associated genes and polypeptides.

[0039] In the present invention, techniques for screening large gene libraries may include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the genes under conditions for detection of a desired activity. Techniques known in the art are amenable to high throughput analysis for screening large numbers of sequences created, e.g., by random mutagenesis techniques. High throughput assays can be followed by secondary screens in order to identify further biological activities which will, e.g., allow one skilled in the art to differentiate agonists from antagonists. The type of a secondary screen used will depend on the desired activity that needs to be tested.

[0040] Drug screening assays are also provided in the present invention. By producing purified and recombinant forms of RA-associated genes and polypeptides of the present invention, or fragments thereof, one skilled in the art can use these to screen for drugs which are either agonists or antagonists of the normal cellular function or their role in cellular signaling. In one aspect, the assay evaluates the ability of a compound to modulate binding between RA-associated genes and polypeptides of the present invention and a naturally occurring ligand. The term “modulating” encompasses enhancement, diminishment, activation or inactivation of activity of RA-associated genes and polypeptides. Assays useful for identifying ligands to RA-associated genes and polypeptides of the present invention are encompassed herein. Such ligands include peptides, proteins, small molecules, and antibodies, which are capable of binding to RA-associated genes and polypeptides of the present invention and modulating their activity. A variety of assay formats may be used in the present invention and are known by those skilled in the art.

[0041] In many drug screening programs which test libraries of compounds and natural extracts, high throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays which are performed in cell-free systems, such as may be derived with purified or semi-purified proteins, are often preferred as primary screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target which is mediated by a test compound.

[0042] Compounds identified using assays, as discussed hereinabove, may be antagonists or agonists of RA-associated genes and polypeptides. These compounds are useful in modulating the activity of RA-associated genes and polypeptides and in treating disorders associated with RA-associated genes and polypeptides.

[0043] “Disorders associated with RA-associated genes and polypeptides” refers to any disorder or disease state in which RA-associated genes and polypeptides play a regulatory role in the metabolic pathway of that disorder or disease. As used herein, the term “treating” refers to the alleviation of symptoms of a particular disorder in a patient, the improvement of an ascertainable measurement associated with a particular disorder, or the prevention of a particular immune, inflammatory or cellular response.

[0044] A compound which acts as a modulator of RA-associated genes and polypeptides may be administered for therapeutic use as a raw chemical or may be the active ingredient in a pharmaceutical formulation. Such formulations of the present invention may contain other therapeutic agents as described below, and may be formulated, for example, by employing conventional solid or liquid vehicles or diluents, as well as pharmaceutical additives of a type appropriate to the mode of desired administration (for example, excipients, binders, preservatives, stabilizers, flavors, etc.) according to techniques such as those well known in the art of pharmaceutical formulation.

[0045] Compounds of the present invention may be administered by any suitable means, for example, orally, such as in the form of tablets, capsules, granules or powders; sublingually; buccally; parenterally, such as by subcutaneous, intravenous, intramuscular, or intrasternal injection or infusion techniques (e.g., as sterile injectable aqueous or non-aqueous solutions or suspensions); nasally such as by inhalation spray; topically, such as in the form of a cream or ointment; or rectally such as in the form of suppositories; in dosage unit formulations containing non-toxic, pharmaceutically acceptable vehicles or diluents.

[0046] Such compounds may, for example, be administered in a form suitable for immediate release or extended release. Immediate release or extended release may be achieved by the use of suitable pharmaceutical compositions comprising compounds of the present invention, or, particularly in the case of extended release, by the use of devices such as subcutaneous implants or osmotic pumps. Compounds of the present invention may also be administered liposomally.

[0047] Exemplary compositions for oral administration include suspensions which may contain, for example, microcrystalline cellulose for imparting bulk, alginic acid or sodium alginate as a suspending agent, methylcellulose as a viscosity enhancer, and sweeteners or flavoring agents such as those known in the art; and immediate release tablets which may contain, for example, microcrystalline cellulose, dicalcium phosphate, starch, magnesium stearate and/or lactose and/or other excipients, binders, extenders, disintegrants, diluents and lubricants such as those known in the art.

[0048] Compounds of the present invention may also be delivered through the oral cavity by sublingual and/or buccal administration. Molded tablets, compressed tablets or freeze-dried tablets are exemplary forms which may be used. Exemplary compositions include those formulating the compound(s) of the present invention with fast dissolving diluents such as mannitol, lactose, sucrose and/or cyclodextrins.

[0049] Also included in such formulations may be high molecular weight excipients such as celluloses (avicel) or polyethylene glycols (PEG). Such formulations may also include an excipient to aid mucosal adhesion such as hydroxy propyl cellulose (HPC), hydroxy propyl methyl cellulose (HPMC), sodium carboxy methyl cellulose (SCMC), maleic anhydride copolymer (e.g., Gantrez), and agents to control release such as polyacrylic copolymer (e.g., Carbopol 934). Lubricants, glidants, flavors, coloring agents and stabilizers may also be added for ease of fabrication and use.

[0050] Exemplary compositions for nasal aerosol or inhalation administration include solutions in saline which may contain, for example, benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, and/or other solubilizing or dispersing agents such as those known in the art.

[0051] Exemplary compositions for parenteral administration include injectable solutions or suspensions which may contain, for example, suitable non-toxic, parenterally acceptable diluents or solvents, such as mannitol, 1,3-butanediol, water, Ringer's solution, an isotonic sodium chloride solution, or other suitable dispersing or wetting and suspending agents, including synthetic mono- or diglycerides, and fatty acids, including oleic acid.

[0052] Exemplary compositions for rectal administration include suppositories which may contain, for example, a suitable non-irritating excipient, such as cocoa butter, synthetic glyceride esters or polyethylene glycols, which are solid at ordinary temperatures, but liquefy and/or dissolve in the rectal cavity to release the drug.

[0053] Exemplary compositions for topical administration include a topical carrier such as Plastibase (mineral oil gelled with polyethylene).

[0054] The effective amount of a compound of the present invention may be determined by one of ordinary skill in the art, and includes exemplary dosage amounts for an adult human of from about 0.1 to 100 mg/kg of body weight of active compound per day, which may be administered in a single dose or in the form of individual divided doses, such as from 1 to 4 times per day. It will be understood that the specific dose level and frequency of dosage for any particular subject may be varied and will depend upon a variety of factors including the activity of the specific compound employed, the metabolic stability and length of action of that compound, the species, age, body weight, general health, sex and diet of the subject, the mode and time of administration, rate of excretion, drug combination, and severity of the particular condition. Preferred subjects for treatment include animals, most preferably mammalian species such as humans, and domestic animals such as dogs, cats and the like, subject to disorders associated with RA-associated genes and polypeptides.

[0055] The compounds of the present invention may be employed alone or in combination with each other and/or other suitable therapeutic agents useful in the treatment of disorders associated with RA-associated genes and polypeptides.

[0056] In another aspect, the present invention relates to the use of an isolated nucleic acid in “antisense” therapy. As used herein, “antisense” therapy refers to administration or in situ generation of oligonucleotides or their derivatives which specifically hybridize under cellular conditions with the cellular mRNA and/or genomic DNA of RA-associated genes so as to inhibit expression of the proteins encoded by such genes, e.g., by inhibiting transcription and/or translation. In general, “antisense” therapy refers to the range of techniques generally employed in the art, and includes any therapy which relies on specific binding to oligonucleotide sequences.

[0057] Gene constructs useful in antisense therapy may be administered may be administered in any biologically effective carrier, e.g., any formulation or composition capable of effectively delivering a nucleic acid sequence to cells in vivo. Approaches include insertion of the subject gene in viral vectors including recombinant retroviruses, adenoviruses, adeno-associated viruses, and herpes simplex virus-1, or recombinant bacterial or eukaryotic plasmids. Viral vectors transfect cells directly; an advantage of infection of cells with a viral vector is that a large proportion of the targeted cells can receive the nucleic acid. Several viral delivery systems are known in the art and can be utilized by one practicing the present invention.

[0058] In addition to viral transfer methods, non-viral methods may also be employed. Most non-viral methods of gene transfer rely on normal mechanisms used by mammalian cells for the uptake and intracellular transport of macromolecules. Exemplary gene delivery systems of this type include liposomal derived systems, poly-lysine conjugates, and artificial viral envelopes. Nucleic acid sequences may also be introduced to cell(s) by direct injection of the gene construct or by electroporation.

[0059] In clinical settings, the gene delivery systems can be introduced into a patient by any of a number of methods, each of which is known in the art. For instance, a pharmaceutical preparation of the gene delivery system can be introduced systemically, e.g., by intravenous injection, and specific transduction of the protein in the target cells occurs predominantly from specificity of transfection provided by the gene delivery vehicle, cell-type or tissue-type expression due to the transcriptional regulatory sequences controlling expression of the receptor gene, or a combination thereof.

[0060] The pharmaceutical preparation of the gene therapy construct can consist essentially of the gene delivery system in an acceptable diluent, or can comprise a slow release matrix in which the gene delivery vehicle is embedded. Alternatively, where the complete gene delivery system can be produced intact from recombinant cells, e.g., retroviral vectors, the pharmaceutical preparation can comprise one or more cells which produce the gene delivery system.

[0061] The following sections sets forth the materials and methods utilized in the present invention.

MATERIALS AND METHODS

[0062] A. Microarray Experimentation

[0063] 1. RNA Isolation

[0064] Human knee biopsy samples were homogenized in 3 ml TRIZOL® Reagent (Life Technologies, Rockville, Md.) and frozen in liquid nitrogen. The samples were thawed, one-third (1ml) of the sample was removed and mixed with 1 ml TRIZOL®. The mixture was then homogenized and snap frozen in liquid nitrogen. Following a thaw, the samples were spun at 14,000 rpm for 10 minutes at 4° C. The supernatants were transferred to new microfuge tubes, extracted with chloroform, and precipitated with isopropanol overnight at −20° C. The RNA was pelleted by centrifugation at 14,000 rpm for 30 minutes. The supernatant was aspirated, and the samples washed two times with 75% ethanol. Following the last spin, the pellets were air-dried, and resuspended in 20 ul of ultra-pure RNase-free water. The RNA samples were further purified using Qiagen RNease mini columns (Qiagen Inc., Valencia Calif.), according to manufacturer's instructions. The RNA was eluted with 50 ul of RNase-free water.

[0065] 2. Probe Preparation

[0066] The RNA was treated in a total reaction volume of 100 ul with RNase Inhibitor (Invitrogen Corp., Carlsbad, Calif.), DNase I (Ambion, Houston, Tex.) for 30 minutes at 37° C. The treated RNA was purified using Qiagen RNease mini columns, according to the manufacturer's instructions.

[0067] For the first strand cDNA synthesis, the RNA was incubated with T7-(dT)24 primer, having the sequence: 5′GGCCAGTGAATTGTAATACGACTCACTATAGGGAGGCGGTTTTTTTT TTTTTTTTTTTTTTTT3′(SEQ ID NO:1) for 10 minutes at 70° C, followed by one minute on ice. First strand buffer, DTT, dNTP and RNase were added, and the samples incubated for 2 minutes at 45° C. Superscript II reverse transcriptase (Invitrogen Corp, Carlsbad, Calif.) was added, and the samples incubated for an additional 60 minutes at 45° C.

[0068] For the second strand synthesis, the first strand cDNA was incubated with second strand buffer, dNTPs, E. coli ligase, E. coli RNase H, E. coli Polymerase I in a total volume of 150 ul for two hours at 16° C. T4 polymerase was added, and the incubation continued for an additional 5 minutes. Following this incubation, EDTA was added, and the samples placed on ice. The cDNA samples were extracted with phenol:chloroform:isoamyl alcohol and precipitated by addition of 0.5 volumes of 7.5 M ammonium acetate and 2.5 volumes of 100% ethanol. The samples were pelleted by a 30 minute room temperature spin at 12,000×g. The pelleted samples were washed with 0.5 ml 80% ethanol, spun for 10 minutes at 12,000×g, and air dried. The samples were resuspended in 12 ul RNase free water.

[0069] The cDNA was labeled using the Enzo Bio Array High Yield RNA transcript labeling kit (Enzo Therapeutics, Farmingdale, N.Y.). The cDNA was incubated with HY reaction buffer, biotin labeled NTP, DTT, RNase mix, and T7 DNA polymerase for six hours at 37° C. Unincorporated nucleotides were removed using Qiagen RNeasy columns according to manufacturer's instructions. The cRNA was fragmented by addition of fragmentation buffer, and incubated for 35 minutes at 95° C. The fragmented cRNA (0.05 mg/ml) was added to a hybridization solution master mix that included 0.1 mg/ml herring sperm DNA, 5 nM oligo B2, 1× standard curve pool, 0.5 mg/ml acetylated BSA, 1×MES hybridization buffer.

[0070] The Affymetrix human U95v2 A, B, and C GeneChips® were probed with the hybridization master mix. The hybridization, washing, and Phycoerythrin streptavidin staining were performed using the Affymetrix hybridization oven and fluidics workstation according to manufacturer's instructions. Stained chips were scanned on the Affymetrix GeneChip scanner, and data was analyzed using the Affymetrix GeneChip software to determine the specifically hybridizing signal for each gene. The differentially expressed genes demonstrated at least a three-fold change in signal when comparing between tissue samples. The differences were all statistically significant (p<0.001) when compared to controls using a T-test.

[0071] Real Time PCR Analysis

[0072] Reverse transcription reactions were performed using up to 3.6 ug mRNA. The RNA was incubated for five minutes at 70° C. and then chilled on ice. A master mix was added containing dNTPs, RT buffer (259 mM Tris-HCl pH 8.3,375 mM KCl, 15 mM MgCl₂), dithiothreitol, random hexamers, RNasin, and reverse transcriptase (Life Technologies, Rockville, Md.). The reactions were incubated for 60 minutes at 37° C., denatured for 5 minutes at 90° C., then chilled on ice for 5 minutes. PCR reactions were performed on ABI Prism® 5700 Sequence Detection System with SYBR green core reagents (PE Applied Biosystem, Foster City, Calif.). All PCR was done at 40 cycles with a pre-incubation period of 50° C. for 2 minutes followed by 95° C. for 10 minutes. Cycling conditions were 95° C. for 15 seconds, 55° C. for 20 seconds, and 75° C. for one minute. Some reactions were done with cycling conditions of 95° C. for 15 seconds and 60° C. for 60 seconds. All data was normalized relative to the signal for the housekeeping gene human hypoxanthine phosphoribosyltransferase I (“HPRT”) (Accession No. BC000578; GI: 12653602) (SEQ ID NO:2), the nucleotide sequence of which is set forth in Table 2, below. TABLE 2 Human Hypoxanthine Phosphoribosyltransferase I: Nucleotide Sequence Accession No. BC000578: GI: 12653602 (SEQ ID NO:2) 1 ggcacgaggc ctcctgagca gtcagcccgc gcgccggccg gctccgttat ggcgacccgc 61 agccctggcg tcgtgattag tgatgatgaa ccaggttatg accttgattt attttgcata 121 cctaatcatt atgctgagga tttggaaagg gtgtttattc ctcatggact aattatggac 181 aggactgaac gtcttgctcg agatgtgatg aaggagatgg gaggccatca cattgtagcc 241 ctctgtgtgc tcaagggggg ctataaattc tttgctgacc tgctggatta catcaaagca 301 ctgaatagaa atagtgatag atccattcct atgactgtag attttatcag actgaagagc 361 tattgtaatg accagtcaac aggggacata aaagtaattg gtggagatga tctctcaact 421 ttaactggaa agaatgtctt gattgtggaa gatataattg acactggcaa aacaatgcag 481 actttgcttt ccttggtcag gcagtataat ccaaagatgg tcaaggtcgc aagcttgctg 541 gtgaaaagga ccccacgaag tgttggatat aagccagact ttgttggatt tgaaattcca 601 gacaagtttg ttgtaggata tgcccttgac tataatgaat acttcaggga tttgaatcat 661 gtttgtgtca ttagtgaaac tggaaaagca aaatacaaag cctaagatga gagttcaagt 721 tgagtttgga aacatctgga gtcctattga catcgccagt aaaattatca atgttctagt 781 tctgtggcca tctgcttagt agagcttttt gcatgtatct tctaagaatt ttatctgttt 841 tgtactttag aaatgtcagt tgctgcattc ctaaactgtt tatttgcact atgagcctat 901 agactatcag ttccctttgg gcggattgtt gtttaacttg taaatgaaaa aattctctta 961 aaccacagca ctattgagtg aaacattgaa ctcatatctg taagaaataa agagaagata 1021 tattagtttt ttaattggta ttttaatttt tatatatgca ggaaagaata gaagtgattg 1081 aatattgtta attataccac cgtgtgttag aaaagtaaga agcagtcaat tttcacatca 1141 aagacagcat ctaagaagtt ttgttctgtc ctggaattat tttagtagtg tttcagtaat 1201 gttgactgta ttttccaact tgttcaaatt attaccagtg aatctttgtc agcagttccc 1261 ttttaaatgc aaatcaataa attcccaaaa atttaaaaaa aaaaaaaaaa aaaaaa

[0073] Primer sets were as follows: HPRT: Forward: GGTATACTGCCTGACCAAGG (SEQ ID NO:3) Reverse: CGAGATGTGATGAAGGAGATGG (SEQ ID NO:4) Name: gi475254 homo sapiens transcription factor ISGF-3 mRNA Forward exon 3 CCCCATGGAAATCAGACAGT (SEQ ID NO:5) Reverse exon 4 TTGCTTTTCCGTATGTTGTG (SEQ ID NO:6) Name: gi28965 human alpha-1-antitrypsin gene (S variant) Forward TGAAGAGCGTCCTGGGTC (SEQ ID NO:7) Reverse CGTCGATGGTCAGCACAG (SEQ ID NO:8) Name: gi5595355 human ADO37 protein Forward GCCCATCAGTGACAGCAAG (SEQ ID NO:9) Reverse CCCAGGCAATGTTGAGGAG (SEQ ID NO:10) Name: gi2185828 human hypothetical protein FLI14834 Forward 417-436 CCTTCCCCTGTCATTGTTC Tm = 58 (SEQ ID NO:11) Reverse 515-534 GACAGTAACCCTGCCACAC Tm = 60 (SEQ ID NO:12) Name: gi183001 human guanylate binding protein isoform I Forward 124-132 GGCGACTGATGGCGAATC Tm = 58 (SEQ ID NO:13) Reverse 264-282 CACCGTGGAGCCCAGAGA Tm = 60 (SEQ ID NO:14) Name: gi2138110 human cysteine dioxygenease Forward 321-341 exon 1 GGCGATGAGGTCAATGTAGA Tm = 60 (SEQ ID NO:15) Reverse 473-493 exon 2 CTGTGTCCTTCACCCCAACA Tm = 62 (SEQ ID NO:16) Name: gi180278 IgG Fc Receptor I Forward GGACACCACAAAGGCAGTGAT (SEQ ID NO:17) Reverse GCAGATGGAGCACCTCACAGT (SEQ ID NO:18) Name: gi1382379 MRP-14 Forward AGCTCAGCTGCTTGTCTGCAT (SEQ ID NO:19) Reverse TTCAAAGAGCTGGTGCGAAA (SEQ ID NO:20) Name: gi1382285 Early B Cell Factor Forward GGCCAGGGCAATGTTATGC (SEQ ID NO:21) Reverse ACATTCTGGCCCTCTGATCCT (SEQ ID NO:22) Name: gi2185828 human hypothetical protein FLI14834 Forward 417-436 CCTTCCCCTGTCATTGTTC (SEQ ID NO:23) Reverse 515-534 GACAGTAACCCTGCCACAC (SEQ ID NO:24)

[0074] B. Further Characterization of GBP-1 (SEO ID NOS. 41 and 42): and GBP-5 (SEO ID NOS. 61 and 62)

[0075] 1. Cell Culture

[0076] For real time PCR analyses, THP-1 cells (10⁷/group) were cultured at 10⁶/ml in RPMI containing 10% heat inactivated fetal calf serum, 2 mM L-glutamine with either medium, BMS-205820 (2 uM), or dexamethasone (100 nM) for 30 minutes at 37° C. in 5% CO₂. LPS was added to each group (100 ng/ml), and the incubation continued for 0.5-8 hr. At the end of each time point, cells were pelleted, washed one time with 10 ml PBS, and stored at −80° C.

[0077] Wild type 3T3 fibroblasts and immortalized fibroblast lines derived from p65 and IkBα germline knockouts were cultured in DMEM with 10% calf serum, glutamax and penicillin/streptomycin. Primary embryonic fibroblasts derived from germline knockouts of relB and p50 were cultured in DMEM with 10% fetal calf serum, glutamax and penicillin/streptomycin. The fibroblasts were plated at 5×10⁵/well of a 6 well plate and cultured overnight at 37° C. in 5% CO₂. Cells were stimulated for 2 or 8 hours with either medium, human TNFα(10 ng/ml) or PMA (10 ng/ml). At each time point, cells were harvested using trypsin/EDTA, washed one time with PBS, and stored at −80° C.

[0078] For the microarray analyses, THP-1 cells (10⁷/group) were cultured at 10⁶/ml as above for 1, 6, 24, or 48 hours with either medium, TNFα(10 ng/ml), IFN-γ(100 U/ml), or LPS (100 ng/ml). At each time point, mRNA was isolated, labeled, and used to probe Affymetrix HG_U95Av2, HG_U95B, and HG_U95C chips.

[0079] Human microvascular endothelial cells from three different donors were obtained from Clonetics (Walkersville, Md.), and cultured in EGM-2 medium (Clonetics). Cells were cultured in 100 mm dishes coated with mouse type IV collagen and allowed to grow to approximately 80% confluency. The cells were then stimulated for 1, 6, or 24 hours with either medium, TNFα(10 ng/ml), or IL-1β(10 ng/ml). At each time point, mRNA was isolated, labeled and used to probe Affymetrix HG_U95Av2 and HG_U95B chips.

[0080] For VEGF and bFGF stimulations, microvascular endothelial cells from three independent donors were obtained, cultured in 100 mm dishes coated with mouse type IV collagen and allowed to grow to 30% confluency. At this time, the media was replaced with DMEM containing 2% fetal calf serum, and the cells were cultured an additional day. The cells were stimulated for 1, 6, or 24 hours with either medium, VEGF (30 ng/ml) or bFGF (10 ng/ml). At each time point, mRNA was isolated, labeled, and used to probe Affymetrix chips as described above.

[0081] Synovial fibroblasts were obtained from Cell Applications, Inc. (San Diego, Calif.), and cultured for 1, 6, or 24 hours with either medium, TNFα(10 ng/ml), IL-1α(10 ng/ml, Peprotech), IL-17 (10 ng/ml, R&D Systems, Minneapolis, Minn.), or IL-17b-Ig fusion protein (5 ng/ml). The IL-17b protein was produced by fusing the full length IL-17b sequence (Shi et al., J. Biol. Chem. 275:19167-19176 (2000)) to the human IgG1 Fc region. At each time point, mRNA was isolated, labeled, and used to probe Affymetrix HG_U95Av2, HG_U95B, HG_U95C, HG_U95D, and HG_U95E chips.

[0082] T cells were isolated from the blood of 4 donors. Lymphocytes were isolated by centrifugation over Accu-prep lymphocyte separation medium (Accurate Chemical and Scientific Corporation, Westbury, N.Y.). The T cells were isolated by rosetting with sheep red blood cells. The isolated T cells were cultured for 6 hours with either medium, or immobilized anti-CD3 (1 ug/ml) plus soluble anti-CD28 (1 ug/ml) antibodies. After 6 hours, mRNA was isolated, labeled, and used to probe Affymetrix HG_U133A and HG_U133B chips.

[0083] 2. cDNA Synthesis for Real Time PCR Analysis

[0084] Total RNA was isolated from cells using the RNeasy® Kit from Qiagen (Valencia, Calif.), including the on-the-column DNase digestion procedure. RNA quality and quantity were evaluated using UV spectrometry. Total RNA was used for first-strand cDNA synthesis using the SuperScript™ First-Strand Synthesis System for RT-PCR (Invitrogen, Carlsbad, Calif.) following the manufacturer's instructions with 50 ng of random hexamers.

[0085] For tissue expression analyses, Human Multiple Tissue cDNA Panel I and Human Immune System MTC Panels were obtained from Clontech (Palo Alto, Calif.). PCR reactions were performed using 2 microliters of cDNA sample (diluted with six microliters of water).

[0086] 3. Primers

[0087] Gene specific primers were designed using the Primer Express software and synthesized by Sigma Genosys (The Woodlands, Tex.).

[0088] Primer sets were as follows: Name: mGBP-1 (SEQ ID NO:82) Forward GGAACAGGAAAGACTTCTCAAGCA (SEQ ID NO:83) Reverse CTTGACGTAGTTGCAAGCTCTCA Name: mGBP-5 (SEQ ID NO:84) Forward GCTGAAGCAAGGTAGCGATGA (SEQ ID NO:85) Reverse CCTCGTTGCTGAGTGTTGGA Name: mHPRT (SEQ ID NO:86) Forward TCAGACTGAAGAGCTACTGTAATGATCA (SEQ ID NO:87) Reverse CAACAATCAAGACATTCTTTCCAGTT Name: hGBP-5 (SEQ ID NO:88) Forward TGCTTTCACTTGTGCCTCTTTC (SEQ ID NO:89) Reverse CAGGCTCTCACAGAGACGGAA Name: hGAPDH (SEQ ID NO:90) Forward AGCCGAGCCACATCGCT (SEQ ID NO:91) Reverse GTGACCAGGCGCCCAATAC

[0089] 3. PCR Assay Conditions

[0090] Reactions were performed in a total volume of 40 μl. The master mix contained SYBR Green I Dye, 50 mM Tris-HCl pH8.3, 75 mM KCl, DMSO, Rox reference dye, 5 mM MgCl₂, 2mM dNTP, Platinum Taq High Fidelity (1U/reaction), and 0.5 μM of each primer. Eight microliters of diluted cDNA was used in each PCR reaction. The amplification program consisted of a 10 minute incubation at 95° C. followed by forty cycles of incubations at 95° C. for 15 seconds and 60° C. for 1 minute. Amplification was followed by melting curve analysis at 60° C. to demonstrate that the amplification was specific to a single amplicon. A negative control without cDNA template was run to assess the overall specificity.

[0091] 4. Data Analysis

[0092] A relative value for the initial target concentration in each reaction was determined using the TaqMan 5700 software. The threshold value was set to 0.5 to obtain cycle threshold values that were used to assign relative message levels for each target. The message levels of hGAPDH were used to normalize all other genes tested from the same cDNA. Message levels from the mouse fibroblast experiment were normalized using mouse HPRT values.

Example 1 Upregulated Genes and Downregulated Genes in RA

[0093] 1. α-1 Antitrypsin Expression

[0094] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of α-1 antitrypsin were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 1. The polynucleotide sequence (SEQ ID NO:25) and amino acid sequence (SEQ ID NO:26) of α-1 antitrypsin are shown in FIGS. 2 and 3, respectively.

[0095] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of α-1 antitrypsin in the RA synovium, the results of which are set forth in Table 3, below. As used in Table 3 and hereinafter, “OA” stands for “Osteoarthritis”. TABLE 3 α-1 antitrypsin: Real Time PCR Results Expression Level T test Normal 1 OA 1.02 0.9574 RA 5.94 0.0034

[0096] α-1 Antitrypsin is the major endogenous inhibitor of the serine protease elastase. It also inhibits other circulating proteases including cathepsin G, thrombin, trypsin, and chymotrypsin. α-1 Antitrypsin is primarily synthesized by the liver. However, neutrophils, monocytes, and alveolar macrophages also increase expression of α-1 antitrypsin in response to proinflammatory stimuli including TNF-α, IL-6 and endotoxin (Knoell, et al., Am. J. Respir. Crit. Care Med. 157:246-255 (1998)). The deficiency of α-1 antitrypsin is associated with connective tissue destruction and the development of emphysema (Crystal, J. Clin. Invest. 85:1343-1352 (1990)).

[0097] At physiological concentrations, (α-1 antitrypsin is a potent stimulator of fibroblast proliferation and collagen production (Dabbagh et al., J. Cell Physiol. 186:73-81 (2001)). High levels of the elastase-α-1 antitrypsin complex have been measured in the serum and synovial fluid of RA patients (Beyeler, et al., J. Rheumatol. 27:15-19 (2000)). α-1 Antitrypsin has also been isolated in a subtraction library examining genes upregulated in monocytes from RA patients (Stuhlmuller, et al., Arthritis Rheum. 43:775-790 (2000)).

[0098] 2. B Lymphocyte Stimulator Expression

[0099] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of B Lymphocyte Stimulator (BLyS, TNSF13B) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 4. The polynucleotide sequence (SEQ ID NO:27) and amino acid sequence (SEQ ID NO:28) of BLyS are shown in FIGS. 5 and 6, respectively.

[0100] BLyS is a member of the TNF family produced by activated T cells, monocytes, and dendritic cells that stimulates B cell expansion and function. Serum BLyS levels have been shown to be elevated in patients with systemic autoimmune diseases, including lupus erythematosus (Zhang, et al., J. Immunol. 166:6-10 (2001)) and RA (Cheema, et al., Arthritis Rheum. 44:1313-1319 (2001)). Mice deficient for the BLyS receptor are resistant to collagen-induced arthritis (Wang, et al., Nature Immunol. 2:632-637 (2001)).

[0101] 3. Fc Gamma RI Expression

[0102] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Fc gamma RI were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 7. The polynucleotide sequence (SEQ ID NO:29) and amino acid sequence (SEQ ID NO:30) of Fc gamma RI are shown in FIGS. 8 and 9, respectively.

[0103] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of Fc gamma RI in the RA synovium, the results of which are set forth in Table 4, below. TABLE 4 Fc gamma RI: Real Time PCR Results Expression Level T test Normal 1 1 OA 1.89 0.35 RA 6.57 0.02

[0104] Fc gamma RI receptors bind IgG immune complexes and trigger cell activation and IL-8 secretion (Salmon, et al., Arthritis Rheum. 44:739-750 (2001)). The expression of Fc gamma RI was increased on monocytes derived from RA patients as compared to healthy controls. A significant correlation between Fc gamma RI, C-reactive protein, and blood platelet count was found in the RA patients. Furthermore, treatment with the steroid prednisolone induced down-regulation of Fc gamma RI expression suggesting that increased expression is associated with disease activity (Torsteinsdottir et al. (1999) Clin. Exp. Immunol. 115:554-560). Mice lacking functional Fc gamma RI and RIII receptors are resistant to collagen-induced arthritis (Kleinau et al. (2000) J. Exp. Med. 191:1611-1616).

[0105] 4. Migration Inhibitory Factor-related Protein 14 Expression

[0106] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Migration inhibitory factor-related protein 14 (MRP-14) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 10. The polynucleotide sequence (SEQ ID NO:31) and amino acid sequence (SEQ ID NO:32) of MRP-14 are shown in FIGS. 11 and 12, respectively.

[0107] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of MRP-14 in the RA synovium, the results of which are set forth in Table 5, below. TABLE 5 MRP-14: Real Time PCR Results Expression Level T test Normal 1 1 OA 0.64 0.49 RA 4.37 0.07

[0108] MRP-14 is a calcium binding protein expressed primarily by circulating neutrophils and monocytes that belongs to the S100 family of proteins (Kerkhoff, et al., Biochim. Biophys. Acta 1448:200-211 (1998); Hessian, et al., J. Leuk. Biol. 53:197-204 (1993)). MRP-14 is strongly expressed by infiltrating neutrophils and monocytes within the inflamed joints of juvenile RA patients (Youssef, et al., J. Rheumatol. 26:2523-2528 (1999)). MRP14 is specifically released during the interaction of monocytes with inflammatory activated endothelium, and is found in high concentrations in the synovial fluid of juvenile RA patients (Frosch, et al., Arthritis Rheum. 43:628-637 (2000)).

[0109] 5. Skin Collagenase Expression

[0110] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Skin Collagenase (MMP-1) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 13. The polynucleotide sequence (SEQ ID NO:33) and amino acid sequence (SEQ ID NO:34) of MRP-14 are shown in FIGS. 14 and 15, respectively.

[0111] MMP-1 is an enzyme that degrades interstitial collagens types I, II, and III. Elevated expression of MMP-1 was detected in synovium from patients with early inflammatory arthritis and with established erosive arthritis. Little expression was detected in normal synovium (Cunnane, et al., Rheumatology 38:34-42 (1999)). Primary cultures of rheumatoid synoviocytes produced MMP-1 as detected using immunohistochemistry. Expression has also been detected in the rheumatoid lesion (Tetlow, et al., Br. J. Rheum. 37:64-70 (1998)).

[0112] 6. Cysteine Dioxygenase Expression

[0113] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of cysteine dioxygenase were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 16. The polynucleotide sequence (SEQ ID NO:35) and amino acid sequence (SEQ ID NO:36) of cysteine dioxygenase are shown in FIGS. 17 and 18, respectively.

[0114] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of Cysteine Dioxygenase in the RA synovium, the results of which are set forth in Table 6, below. TABLE 6 Cysteine Dioxygenase: Real Time PCR Results Expression Level T test Normal 1 OA 1.21 0.77 RA 0.19 0.06

[0115] Cysteine dioxygenase is an enzyme involved in sulphate metabolism whose activity has been shown to be decreased in RA patients (Bradley, et al., J. Rheumatol. 21:1192-1196 (1994)).

Example 2 Upregulated Genes and Downregulated Genes in RA

[0116] 1. HLA-DR2/Dw12 Expression

[0117] Using the materials and methods described hereinabove (Materials and Methods, Section A), significant increases in expression of HLA-DR2/Dw12 were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 19. The polynucleotide sequence (SEQ ID NO:37) and amino acid sequence (SEQ ID NO:38) of HLA-DR2/Dw12 are shown in FIGS. 20 and 21, respectively.

[0118] Upregulation of MHC class II alleles, specifically HLA-DRB1 and HLA-DR4 subtypes, has previously been associated with development of RA (Kerlan-Candon, et al., Arthritis Rheum. 44:1281-1292 (2001)). Evidence suggests that expression of the DRB1*0401 and related haplotypes predisposes individuals to RA (Nepom, Adv. Immunol. 68:315-332 (1998)). This allele is also associated with the most severe form of RA leading to extraarticular manifestations (Weyand, et al., J. Clin. Invest. 89:2033-2039 (1992)). Specific associations of HLA-DR2 expression with RA, shown in the present invention, have not been previously demonstrated.

[0119] 2. Stimulator of Iron Transport Expression

[0120] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Stimulator of Iron Transport were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 22. The polynucleotide sequence (SEQ ID NO:39) and amino acid sequence (SEQ ID NO:40) of Stimulator of Iron Transport are shown in FIGS. 23 and 24, respectively.

[0121] Stimulator of Iron Transport is a regulator of ferric and ferrous iron uptake (Yu et al., J. Biol. Chem. 273:21380-21385 (1998); Gutierrez, et al., J. Cell Biol. 139:895-905 (1997)).

[0122] 3. Guanylate Binding Protein Isoform 1 Expression

[0123] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Guanylate Binding Protein Isoform 1 (GBP-1) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 25. The polynucleotide sequence (SEQ ID NO:41) and amino acid sequence (SEQ ID NO:42) of GBP-1 are shown in FIGS. 26 and 27 respectively.

[0124] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of GBP-1 in the RA synovium, the results of which are set forth in Table 7, below. TABLE 7 Guanylate Binding Protein Isoform 1: Real Time PCR Results Expression Level T test Normal 1 OA 1.00 0.985 RA 3.89 0.003

[0125] GBP-1 is an interferon-inducible protein that binds guanine nucleotides and possesses GTPase activity (Cheng, et al., Mol. Cell. Biol. 11:4717-4725 (1991)).

[0126] The regulation of GBP-1 was further characterized using the materials and methods described hereinabove (Materials and Methods, Section B), the results of which are set forth in Example 3 below.

[0127] 4. ISGF-3 p91 (STAT1) Expression

[0128] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of ISGF-3 p91 (STAT1) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 28. The polynucleotide sequence (SEQ ID NO:43) and amino acid sequence (SEQ ID NO:44) of ISGF-3 p91 (STAT1) are shown in FIGS. 29 and 30, respectively.

[0129] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of ISGF-3 p91 in the RA synovium, the results of which are set forth in Table 8, below. TABLE 8 ISGF-3 p91: Real Time PCR Results Expression Level T test Normal 1 OA 0.93 0.720 RA 3.91 0.002

[0130] ISGF-3 p91 (STAT1) is a transcription factor involved in interferon signaling pathways (Schindler, et al., Proc. Nat. Acad. Sci. 89:7836-7839 (1992)). Continuous activation of STAT1 has been seen in synovial fluid cells derived from RA but not osteoarthritis patients (Yokota, et al., J. Rheumatol. 28:1952- 1959 (2001)).

[0131] 5. Mad Protein Homolog-3 Expression

[0132] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Mad Protein Homolog (MAD-3) were detected in the RA synovium. MAD-3 is also known as Mothers Against Decapentaplegic Homolog 3 (Smad-3). This decreased expression is shown in the microarray data in FIG. 31. The polynucleotide sequence (SEQ ID NO:45) and amino acid sequence (SEQ ID NO:46) of MAD-3 are shown in FIGS. 32 and 33, respectively.

[0133] Mad-3 is an intracellular mediator downstream of the TGF-β/activin receptors that appears to be important for monocyte chemotaxis in response to TGF-β (Zhang, et al., Nature 383:168-172 (1996); Ashcroft, et al., Nature Cell Biol. 1:260-266 (1999).

[0134] 6. Human Transforming Growth Factor-Beta Type III Receptor Expression

[0135] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Human Transforming Growth Factor-Beta Type III Receptor (TGF-β type III receptor) were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 34. The polynucleotide sequence (SEQ ID NO:47) and amino acid sequence (SEQ ID NO:48) of TGF-β type III receptor are shown in FIGS. 35 and 36, respectively.

[0136] 7. Early B Cell Factor Expression

[0137] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Early B Cell Factor (EBF) were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 37. The polynucleotide sequence (SEQ ID NO:49) and amino acid sequence (SEQ ID NO:50) of EBF are shown in FIGS. 38 and 39, respectively.

[0138] Using the materials and methods described hereinabove (Materials and Methods, Section A), Real Time PCR was conducted to quantify the expression of EBF in the RA synovium, the results of which are set forth in Table 9, below. TABLE 9 EBF: Real Time PCR Results Expression Level T test Normal 1 1 OA 0.72 0.66 RA 0.20 0.05

[0139] EBF is a transcription factor required for B cell differentiation (Gisler, et al., Blood 96:1457-1464 (2000)).

[0140] 8. Duodenal Cytochrome b Expression

[0141] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Duodenal Cytochrome b were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 40. The polynucleotide sequence (SEQ ID NO:51) and amino acid sequence (SEQ ID NO:52) of Duodenal Cytochrome b are shown in FIGS. 41 and 42, respectively.

[0142] Duodenal cytochrome b is a protein localized to the duodenal mucosa possessing ferric reductase activity (McKie, et al., Science 291:1755-1759 (2001)).

[0143] 9. Nuclear LIM Interactor-Interacting Factor Expression

[0144] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Nuclear LIM Interactor-Interacting Factor (NLI-IF) were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 43. The polynucleotide sequence (SEQ ID NO:53) and amino acid sequence (SEQ ID NO:54) of NLI-IF are shown in FIGS. 44 and 45, respectively.

[0145] The NLI-IF amino acid sequence has homology to the nuclear Lim interactor interacting factor from Gallus gallus. It is one of a family of four related proteins of unknown function (Marquet, et al., Mamm. Genome 11:755-762 (2000)).

[0146] 10. Deleted in Liver Cancer 1 Expression

[0147] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of Deleted in Liver Cancer 1 (DLC1) were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 46. The polynucleotide sequence (SEQ ID NO:55) and amino acid sequence (SEQ ID NO:56) of DLC1 are shown in FIGS. 47 and 48, respectively.

[0148] DLC1 is a candidate tumor suppressor gene possessing a high degree of sequence similarity to the rat p122 RhoGap gene (Yuan, et al., Cancer Res. 58:2196-2199 (1998); Ng, et al., Cancer Res. 60:6581-6584 (2000)).

[0149] 11. GI: 12005907

[0150] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of the polynucleotide identified by Genbank Accession No. AF260335 (GI: 12005907) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 49. The polynucleotide sequence (SEQ ID NO:57) and amino acid sequence (SEQ ID NO:58) are shown in FIGS. 50 and 51, respectively.

[0151] Further, Real Time PCR was conducted to quantify the expression of this polynucleotide in the RA synovium, the results of which are set forth in Table 10. TABLE 10 GI: 12005907: Real Time PCR Results Expression Level T test Normal 1 OA 1.44 0.34 RA 2.39 0.04

[0152] 12. Apolipoprotein L Expression

[0153] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Apolipoprotein L (APOL) (Genbank Accession No. NM_(—)003661) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 52. The polynucleotide sequence (SEQ ID NO:59) and amino acid sequence (SEQ ID NO:60) of APOL are shown in FIGS. 53 and 54, respectively.

[0154] Apolipoprotein L is a component of human plasma lipoproteins (Duchateau, et al., J. Biol. Chem. 272:25576-25582 (1997)).

[0155] 13. Homo Sapiens Guanylate Binding Protein 5 Expression

[0156] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Homo Sapiens Guanylate Binding Protein 5 (Genbank Accession No. AF288815) (GBP-5) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 55. The polynucleotide sequence (SEQ ID NO:61) and amino acid sequence (SEQ ID NO:62) of Homo Sapiens GBP-5 are shown in FIGS. 56 and 57, respectively. GBP-5 is highly homologous to GBP-1 described above (SEQ ID NO: 42).

[0157] The regulation of GBP-5 was further characterized using the materials and methods described hereinabove (Materials and Methods, Section B), the results of which are set forth in Example 3 below.

[0158] 14. Human Proteasome Activator HPA28 Subunit Beta Expression

[0159] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of HPA28 subunit beta (HPA28) (Genbank Accession No. D45248) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 58. The polynucleotide sequence (SEQ ID NO:63) and amino acid sequence (SEQ ID NO:64) of HPA28 are shown in FIGS. 59 and 60, respectively.

[0160] HPA28 beta subunits associate with alpha subunits to form PA28, an activator of the 20S proteasome. Both subunits are coordinately regulated by interferon-γ (Ahn, et al., FEBS Lett. 366:37-42 (1995)).

[0161] 15. Homo Sapiens FYN Binding Protein

[0162] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Homo Sapiens FYN Binding Protein (Genbank Accession No. AF001862) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 61. The polynucleotide sequence (SEQ ID NO:65) and amino acid sequence (SEQ ID NO:66) of Homo Sapiens FYN Binding Protein are shown in FIGS. 62 and 63, respectively.

[0163] FYN Binding Protein is a hematopoietic specific adapter protein that associates in a T cell receptor-inducible manner with another hematopoietic-specific adapter, SLP-76 (daSilva, et al., Proc. Natl. Acad. Sci. USA 94:7493-7498 (1997)). T cells from mice lacking FYN Binding Protein exhibit impaired proliferative responses and impaired integrin clustering following T cell receptor crosslinking (Peterson, et al., Science 293:2263-2265 (2001)).

[0164] 16. VAMP5

[0165] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of VAMP5 (GI:4027902) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 64. The polynucleotide sequence (SEQ ID NO:67) and amino acid sequence (SEQ ID NO:68) of VAMP5 are shown in FIGS. 65 and 66, respectively.

[0166] VAMP5 is a novel synaptobrevin protein that is preferentially expressed in skeletal muscle and heart. Its expression is increased during myogenesis and it localizes to the plasma membrane as well as intracellular perinuclear and peripheral vesicular structures of myotubes (Zeng, et al., Mol. Biol. Cell 9:2423-2437 (1998)).

[0167] 17. GI: 2466183

[0168] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of the polynucleotide identified by GI:2466183 were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 67. The sequence of this polynucleotide is shown in FIG. 68 (SEQ ID NO:69).

[0169] 18. GI: 22192831

[0170] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of the polynucleotide identified by GI: 2219283 were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 69. The sequence of this polynucleotide is shown in FIG. 70 (SEQ ID NO:70).

[0171] 19. Hypothetical Protein FLJ20152 (GI: 9506660)

[0172] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of the Hypothetical Protein FLJ20152 identified by GI: 9506660 were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 71. The polynucleotide sequence (SEQ ID NO:71) and amino acid sequence (SEQ ID NO:72) of Hypothetical Protein FLJ20152 are shown in FIGS. 72 and 73, respectively.

[0173] 20. GI: 5876137

[0174] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of the polynucleotide identified by GI: 5876137 were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 74. The sequence of this polynucleotide is shown in FIG. 75 (SEQ ID NO:73).

[0175] 21. GI: 2185828

[0176] Using the materials and methods described hereinabove (Materials and Methods, Section A), decreases in expression of the polynucleotide identified by GI: 2185828 were detected in the RA synovium. This decreased expression is shown in the microarray data in FIG. 76. The polynucleotide sequence (SEQ ID NO:74) and amino acid sequence (SEQ ID NO:75) are shown in FIGS. 77 and 78, respectively.

[0177] Further, Real Time PCR was conducted to quantify the expression of this polynucleotide in the RA synovium, the results of which are set forth in Table 11. TABLE 11 GI: 2185828 Real Time PCR Results Expression Level T test Normal 1 OA 0.87 0.632 RA 0.21 0.014

[0178] 22. Homo Sapiens Proteasome (Prosome, Macropain) Subunit, Beta Type, 9

[0179] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of the Homo sapiens proteasome (prosome, macropain) subunit, beta type, 9 (GI: 14754802) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 79. The polynucleotide sequence (SEQ ID NO:76) and amino acid sequence (SEQ ID NO:77) of homo sapiens proteasome (prosome, macropain) subunit, beta type, 9 are shown in FIGS. 80 and 81, respectively.

[0180] The of homo sapiens proteasome (prosome, macropain) subunit, beta type, 9 is encoded by a gene within the major histocompatibility complex. This subunit replaces beta subunit PSMB6 following interferon gamma stimulation, thereby altering the proteasome specificity.

[0181] 23. TYRO Protein Tyrosine Kinase Binding Protein (TYROBP); GI:4507754

[0182] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of the TYRO protein tyrosine kinase binding protein (TYROBP) (GI:4507754) were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 82. The polynucleotide sequence (SEQ ID NO:78) and amino acid sequence (SEQ ID NO:79) are shown in FIGS. 83 and 84, respectively.

[0183] TYRO protein tyrosine binding protein (TYROBP) is an ITAM-bearing transmembrane adaptor protein that associates non-covalently with receptors in natural killer and myeloid cells (Lanier, et al., Nature 391:703-707 (1998)). Mice deficient for TYROBP have normal lymphoid and myeloid development, however activating Ly49 receptors on NK cells are downregulated and nonfunctional. The TYROBP deficient mice are resistant to induction of experimental autoimmune encephalomyelitis and exhibit decreased interferon-γ production by antigen-primed CD4+ T cells due to inadequate T cell priming in vivo (Bakker, et al., Immunity 13:345-353 (2000)). Humans expressing loss of function mutations in TYROBP exhibit presenile dementia with bone cysts (Paloneva, et al., Nat. Genet. 25:357-361 (2000)).

[0184] 24. Interleukin 15 Receptor, Alpha

[0185] Using the materials and methods described hereinabove (Materials and Methods, Section A), increases in expression of Interleukin 15 Receptor, alpha were detected in the RA synovium. This increased expression is shown in the microarray data in FIG. 85. The polynucleotide sequence (SEQ ID NO:80) and amino acid sequence (SEQ ID NO:81) are shown in FIGS. 86 and 87, respectively.

[0186] IL-15 is a T cell growth factor that shares many functional similarities with IL-2. The IL-15 receptor consists of a high affinity binding alpha chain and the common IL-2 receptor beta and gamma chains (Anderson, et al., J. Biol. Chem. 270:29862-29869 (1995)). Elevated levels of IL-15 have been detected in the serum from systemic lupus erythematosus patients (Aringer, et al., Rheumatology 40:876-881 (2001)), in the synovial tissue of rheumatoid arthritis patients (Thurkow, et al., J. Pathol. 181:444-450 (1997)), and in synovial fluid from rheumatoid arthritis patients (McInnes, et al., Nat. Med. 2:175-182 (1996)). Administration of soluble IL-15 receptor alpha chain to mice prevented collagen-induced arthritis (Ruchatz, et al., J. Immunol. 160:5654-5660 (1998)), suggesting that IL-15 plays a role in the development of rheumatoid arthritis. Upregulation of the IL-15 receptor alpha chain in rheumatoid arthritis has not been previously described.

[0187] Example 3

Characterization of RA-Associated Genes GBP-1 and GBP5

[0188] As stated above, GBP-1 and GBP-5 were further characterized using the materials and methods set forth above (Materials and Methods, Section B).

[0189] GBP-1 has been identified as an interferon-inducible protein in human fibroblasts (Cheng et al., J. Biol. Chem. 258:7746-7750 (1983)). GBP-1 mRNA has been shown to be induced in endothelial cells in response to the pro-inflammatory stimuli, TNFα and IL-1α (Guenzi et al., EMBO J. 20:5568-5577 (2001)). This study also suggested that GBP-1 mediates the anti-proliferative effects of these cytokines.

[0190] As TNFα and IL-1α are known to activate the transcription factor NF-kB, it was determined whether NF-kB was required for induction of GBP-1 and GBP-5 in the human THP-1 monocyte line. THP-1 monocytes were stimulated with lipopolysaccharide (LPS), a known inducer of NF-kB, in the presence and absence of a selective peptide inhibitor of NF-kB nuclear translocation, which is set forth in Fujihara et al., J. Immunol. 165:1004-1012 (2000) and designated “BMS-205820”.

[0191] Following a 2 hour stimulation, RNA was isolated from 2 sets of independently treated THPs, and real time PCR was performed using primers specific for either GBP-1 or GBP-5, as shown in FIG. 88. Treatment of THP-1 cells with LPS significantly increased steady-state mRNA levels of both GBP-1 (FIGS. 88A and 88B) and GBP-5 (FIGS. 88C and 88D). Expression of both genes was significantly inhibited by BMS-205820, suggesting that LPS-mediated induction of GBP-1 and GBP-5 expression is dependent on NF-kB activity.

[0192] An extended time course was performed to further characterize GBP-1 and GBP-5 expression, as shown in FIG. 89. THP-1 cells were stimulated for 0.5, 1, 4, 6, and 8 hours with LPS. Some groups included either BMS-205820 or the steroid dexamethasone for 2 or 6 hours. Dexamethasone is also known to inhibit NF-KB activity (Scheinman et al., Mol. Cell. Biol. 15:943-953 (1995)). At each time point, mRNA was isolated and real time PCR was performed using primers specific for either GBP-1 FIG. 89A) or GBP-5 (FIG. 89B). Steady state mRNA levels for both GBP-1 and GBP-5 peaked at 6 hours post stimulation. Addition of either BMS-205820 or dexamethasone significantly inhibited mRNA induction of both genes at 2 and 6 hours. The ability of two different NF-kB inhibitors to block GBP-1 and GBP-5 expression further confirms that LPS-mediated induction of these genes is dependent on NF-kB activity.

[0193] To further confirm that GBP-1 and GBP-5 are NF-kB target genes, expression in mouse embryonic fibroblasts derived from germline knockouts of members of the NF-kB family was examined (FIG. 90). Wild type 3T3 cells, embryonic fibroblasts derived from knockouts of p65, RelB, p50, and IkBα were stimulated for 2 or 8 hours with either TNFα or PMA. At each time point, mRNA was isolated and real time PCR was performed using primers specific for either mouse GBP-1 (FIG. 90A) or GBP-5 (FIG. 90B). Stimulation with TNF(α but not PMA induced increased steady-state levels of both GBP-1 and GBP-5 mRNA. Induction of GBP-1 mRNA was completely ablated in cells lacking either p65 or RelB. GBP-1 mRNA was superinduced in cells lacking either p50 or IkBα, suggesting that these proteins negatively regulate GBP-1 mRNA. IkBα is a known inhibitor of NF-kB activity (Baeuerle et al., Science 242:540-545 (1988)). Homodimers of p50 have also been shown to repress certain genes (Plaksin et al., J. Exp. Med. 177:1651-1662 (1993)).

[0194] Similar to GBP-1, induction of GBP-5 mRNA was completely ablated in cells lacking p65. In contrast to GBP-1, GBP-5 mRNA was superinduced in cells lacking RelB. Similar to GBP-1, GBP-5 mRNA was also superinduced in cells lacking either p50 or IkBα. These data suggest that p65 expression is required for the induction of both GBP-1 and GBP-5. Complexes containing RelB appear to differentially regulate GBP-1 and GBP-5 expression. Taken together, these data are consistent with NF-kB-dependent regulation of GBP-1 and GBP-5 expression.

[0195] The tissue expression profiles of GBP-1 and GBP-5 were further characterized. Human tissue cDNA panels were analyzed by real time PCR with primers selective for GBP-1 (FIG. 91A) and GBP-5 (FIG. 91B). Both genes had very similar patterns of expression. The highest steady state mRNA levels were detected in hematopoietic tissues including spleen, peripheral blood leukocytes, and lymph nodes. Lower levels of expression were detected in lung, followed by liver, thymus, tonsil, bone marrow, placenta, fetal liver, tonsil, and pancreas.

[0196] Based on the high expression detected in hematopoietic tissue, the expression of GBP-1 and GBP-5 in panels of resting and stimulated immune cells was examined. Consistent with the identification of GBP-1 as an interferon response gene (Cheng et al., J. Biol. Chem. 258:7746-7750 (1983)), steady state levels of GBP-1 and GBP-5 mRNA were strongly induced by interferon-γ treatment of THP-1 monocytes, as shown in FIGS. 92A and 92B. Much lower levels of expression were induced by TNFα and LPS.

[0197] Consistent with published reports (Guenzi et al., EMBO J. 20:5568-5577 (2001)), GBP-1 expression was strongly induced by TNFα and IL-1β in human microvascular endothelial cells (FIG. 93A). No induction was seen in response to either VEGF or basic FGF. In contrast to GBP-1, induction of GBP-5 by TNFα and IL-1β was variable (FIG. 93B). Cells from two out of three donors upregulated GBP-5 mRNA in response to TNFα. Only one donor significantly induced GBP-5 mRNA in response to IL-1β.

[0198] Synovial fibroblasts derived from rheumatoid arthritis patients were stimulated with either TNFα, IL-1α, IL-17, or IL-17b. GBP-1 mRNA was induced at 1 and 6 hours by stimulation with either TNFα or IL-1α, but not in response to either IL-17 or IL-17b (FIG. 94A). Low levels of GBP-5 expression were detected in synovial fibroblasts (FIG. 94B). Induction of GBP-5 in response to the different stimuli was variable and not sustained.

[0199] GBP-1 and GBP-5 had similar patterns of expression in T cells (FIG. 95). Peripheral blood T cells were isolated from 4 different donors and stimulated for 6 hours with antibodies to CD3 and CD28 as a mimic of antigen stimulation. Steady state levels of GBP-1 (FIG. 95A) and GBP-5 (FIG. 95B) mRNA were strongly induced by antigen receptor crosslinking.

[0200] The induction of GBP-1 and GBP-5 by pro-inflammatory stimuli including LPS, IL-1, TNFα, and antigen receptor crosslinking is consistent with NF-kB-dependent regulation of these genes. Overexpression of these genes in synovium from rheumatoid arthritis patients is also consistent with NF-kB-dependent regulation. NF-kB is activated in the inflamed synovium of rheumatoid arthritis patients (Marok et al., Arthritis Rheum. 39:583-591 (1996)) and animal models of arthritis (Miagkov et al., Proc. Natl. Acad. Sci. USA 95:13859-13864 (1998)). The regulation of GBP-1 and GBP-5 by NF-kB coupled with the involvement of NF-kB in the development of arthritis indicates that these genes play a role in disease pathology.

[0201] While the invention has been described in connection with specific embodiments therefore, it will be understood that it is capable of further modifications and this application is intended to cover any variations, uses, or adaptations of the invention following, in general, the principles of the invention and including such departures from the present disclosure as come within known or customary practice within the art to which the invention pertains and as may be applied to the essential features hereinbefore set forth and as follows in the scope of the appended claims. All references cited herein are expressly incorporated in their entirety. 

What is claimed is:
 1. An assay for identifying a compound that modulates the activity of a gene associated with rheumatoid arthritis, comprising: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein the nucleic acid sequence of said gene associated with rheumatoid arthritis is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73 and SEQ ID NO:74; (2) contacting said cell expressing said gene associated with rheumatoid arthritis with a test compound; and (3) determining whether said test compound modulates the activity of said gene associated with rheumatoid arthritis.
 2. The assay of claim 1, wherein said assay is a cell-based assay.
 3. The assay of claim 1, wherein said assay is a cell-free assay.
 4. The assay of claim 3, wherein said cell-free assay is a ligand-binding assay.
 5. The assay of claim 1, wherein said test compound modulates the activity of said gene associated with rheumatoid arthritis.
 6. The assay of claim 1, wherein said test compound is an antagonist of a gene associated with rheumatoid arthritis.
 7. The assay of claim 1, wherein said test compound is an agonist of a gene associated with rheumatoid arthritis.
 8. The assay of claim 1, wherein said test compound binds to said gene associated with rheumatoid arthritis.
 9. The assay of claim 1, wherein said assay is useful for identifying compounds which are useful for the treatment of rheumatoid arthritis.
 10. An assay for identifying a compound that modulates the activity of a protein associated with rheumatoid arthritis, comprising: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein said gene encodes a polypeptide having an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72 and SEQ ID NO:75; (2) contacting said cell expressing said gene associated with rheumatoid arthritis with a test compound; and (3) determining whether said test compound modulates the activity of said protein associated with rheumatoid arthritis.
 11. The assay of claim 10, wherein said assay is a cell-based assay.
 12. The assay of claim 10, wherein said assay is a cell-free assay.
 13. The assay of claim 12, wherein said cell-free assay is a ligand-binding assay.
 14. The assay of claim 10, wherein said test compound modulates the activity of said polypeptide associated with rheumatoid arthritis.
 15. The assay of claim 10, wherein said test compound is an antagonist of a polypeptide associated with rheumatoid arthritis.
 16. The assay of claim 10, wherein said test compound is an agonist of a polypeptide associated with rheumatoid arthritis.
 17. The assay of claim 10, wherein said test compound binds to said polypeptide associated with rheumatoid arthritis.
 18. The assay of claim 10, wherein said assay is useful for identifying compounds which are useful for the treatment of rheumatoid arthritis.
 19. A method for the treatment of rheumatoid arthritis, comprising: (1) identifying a patient suffering from rheumatoid arthritis; and (2) administering to said patient a therapeutically effective amount of a modulator of a gene associated with rheumatoid arthritis, wherein said gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73 and SEQ ID NO:74.
 20. The method of claim 19, wherein said patient is identified as suffering from rheumatoid arthritis by measuring the expression level of said gene associated with rheumatoid arthritis in said patient.
 21. The method of claim 19, wherein said modulator is an antagonist of a gene associated with rheumatoid arthritis.
 22. A method for the treatment of rheumatoid arthritis, comprising: (1) identifying a patient suffering from rheumatoid arthritis; and (2) administering to said patient suffering from rheumatoid arthritis a therapeutically effective amount of a modulator of a polypeptide associated with rheumatoid arthritis, wherein said polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72 and SEQ ID NO:75.
 23. The method of claim 22, wherein said patient is identified as suffering from rheumatoid arthritis by measuring the expression level of said polypeptide associated with rheumatoid arthritis.
 23. The method of claim 22, wherein said modulator is an antagonist of a polypeptide associated with rheumatoid arthritis.
 24. A method for the prevention of rheumatoid arthritis, comprising: (1) identifying a patient at risk for rheumatoid arthritis; and (2) administering to said patient at risk for rheumatoid arthritis a therapeutically effective amount of a modulator of a gene associated with rheumatoid arthritis, wherein said gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73 and SEQ ID NO:74.
 25. The method of claim 24, wherein said patient is identified as being at risk for rheumatoid arthritis by measuring the expression level of said gene associated with rheumatoid arthritis in said patient.
 26. The method of claim 24, wherein said modulator is an antagonist of said gene associated with rheumatoid arthritis.
 27. A method for the prevention of rheumatoid arthritis, comprising: (1) identifying a patient at risk for rheumatoid arthritis; and (2) administering to said patient at risk for rheumatoid arthritis a therapeutically effective amount of a modulator of a polypeptide associated with rheumatoid arthritis, wherein said polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72 and SEQ ID NO:75.
 28. The method of claim 27, wherein said patient is identified as being at risk for rheumatoid arthritis by measuring the expression level of said polypeptide associated with rheumatoid arthritis in said patient.
 29. The method of claim 27, wherein said modulator is an antagonist of said polypeptide associated with rheumatoid arthritis.
 30. A compound useful for the treatment of rheumatoid arthritis, wherein said compound is identified by: (1) providing a cell expressing a gene associated with rheumatoid arthritis, wherein said gene associated with rheumatoid arthritis has a nucleic acid sequence which is at least 95% identical to a nucleic acid sequence selected from the group consisting of SEQ ID NO:37, SEQ ID NO:39, SEQ ID NO:41, SEQ ID NO:43, SEQ ID NO:45, SEQ ID NO:47, SEQ ID NO:49, SEQ ID NO:51, SEQ ID NO:53, SEQ ID NO:55, SEQ ID NO:57, SEQ ID NO:59, SEQ ID NO:61, SEQ ID NO:63, SEQ ID NO:65, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:70, SEQ ID NO:71, SEQ ID NO:73 and SEQ ID NO:74; (2) contacting said cell expressing said gene associated with rheumatoid arthritis with said compound; and (3) determining whether said compound modulates the activity of said gene associated with rheumatoid arthritis.
 31. The compound of claim 30, wherein said compound is an antagonist of said gene associated with rheumatoid arthritis.
 32. The compound of claim 30, wherein said compound is an agonist of said gene associated with rheumatoid arthritis.
 33. A compound useful for the treatment of rheumatoid arthritis, wherein said compound is identified by: (1) providing a cell expressing a polypeptide associated with rheumatoid arthritis, wherein said polypeptide associated with rheumatoid arthritis has an amino acid sequence which is at least 95% identical to an amino acid sequence selected from the group consisting of SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID NO:44, SEQ ID NO:46, SEQ ID NO:48, SEQ ID NO:50, SEQ ID NO:52, SEQ ID NO:54, SEQ ID NO:56, SEQ ID NO:58, SEQ ID NO:60, SEQ ID NO:62, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:68, SEQ ID NO:72 and SEQ ID NO:75; (2) contacting said cell expressing said polypeptide associated with rheumatoid arthritis with said compound; and (3) determining whether said compound modulates the activity of said polypeptide associated with rheumatoid arthritis.
 34. The compound of claim 33, wherein said compound is an antagonist of said polypeptide associated with rheumatoid arthritis.
 35. The compound of claim 30, wherein said compound is an agonist of said polypeptide associated with rheumatoid arthritis. 